1. Mapping functional connectivity based on synchronized CMRO2 fluctuations during the resting state Synchronized low-frequency fluctuations in the resting state fMRI signal have been suggested to be associated with functional connectivity in brain networks. However, the underlying mechanism of this connectivity is still poorly understood. In this study, we examined spontaneous fluctuations at the level of cerebral metabolic rate of oxygenation (CMRO2), an index reflecting regional oxygen consumption and metabolism, and thus less sensitive to vascular dynamics. The CMRO2 signal was obtained based on a biophysical model with data acquired from simultaneous blood oxygenation level dependent (BOLD) and perfusion signals. CMRO2-based functional connectivity maps were generated in three brain networks: visual, default-mode, and hippocampus. Experiments were performed on twelve healthy participants during 'resting state'and as a comparison, with a visual task. CMRO2 signals in each of the abovementioned brain networks showed significant correlations. Functional connectivity maps from the CMRO2 signal are, in general, similar to those from BOLD and perfusion. This study provides evidence that the spontaneous fluctuations in fMRI at rest likely originate from dynamic changes of cerebral metabolism reflecting neuronal activity. (NeuroImage 45:694-701, 2009) 2. Static and dynamic characteristics of cerebral blood flow during the resting state In this study, the static and dynamic characteristics of cerebral blood flow (CBF) in the resting state were investigated using an arterial spin labeling (ASL) perfusion imaging technique. Consistent with previous PET results, static CBF measured by ASL was significantly higher in the posterior cingulate cortex (PCC), thalamus, insula/superior temporal gyrus (STG) and medial prefrontal cortex (MPFC) than the average CBF of the brain. The dynamic measurement of CBF fluctuations showed high correlation (functional connectivity) between components in the default mode network. These brain regions also had high local temporal synchrony and high fluctuation amplitude, as measured by regional homogeneity (ReHo) and amplitude of low-frequency fluctuation (ALFF) analyses. The spatial pattern of the static CBF correlated well with that of the dynamic indices. The high static and dynamic activities suggest that these regions play a vital role in maintaining and facilitating fundamental brain functions. (NeuroImage 48:515-524, 2009) 3. Functional connectivity between the thalamus and visual cortex under eyes closed and eyes open conditions: A resting-state fMRI study The thalamus and visual cortex are two key components associated with the alpha power of electroencephalography. However, their functional relationship remains to be elucidated. Here, we employ resting-state functional MRI to investigate the temporal correlations of spontaneous fluctuations between the thalamus and visual cortex under both eyes open and eyes closed conditions. The whole thalamus show negative correlations with the visual cortex and positive correlations with its contralateral counterpart in eyes closed condition, but which are significantly decreased in eyes open condition, consistent with previous findings of electroencephalography desynchronization during eyes open resting state. Furthermore, we find that bilateral thalamic mediodorsal nuclei and bilateral ventrolateral nuclei have remarkably similar connectivity maps, and resemble to those of the whole thalamus, suggesting their crucial contributions to the thalamus-visual correlations. Our data provides evidence for the associations of intrinsic spontaneous neuronal activity between the thalamus and visual cortex under different resting conditions. (Hum. Brain Mapp. 30, 3066-3078, 2009) 4. Improvement of T1 measurement accuracy Recently, we observed the discrepancy of the signal intensities from a multi-slice inversion recovery (IR) Look-Locker echo-planar imaging (LL-EPI) sequence with and without fat saturation (FS) preparation (prep) pulses. It is suspected that the FS pulses, which were frequency selective but not spatial selective, induced such signal loss by magnetization transfer contrast (MTC). This unexpected (and undesirable) signal attenuation by FS prep pulses in multi-slice imaging would be problematic especially in quantitative MR imaging, such as relaxation time constant (T1) measurement. We investigated MTC by the FS pulses in multi-slice LL-EPI. A reduction of signal intensity and bias on T1 measurement caused by the FS prep pulses were demonstrated varying imaging parameters. As a solution, water-only excitation (WE) pulses, with spatial and spectral selection, showed the potential to minimize the signal attenuation and provide the unbiased T1 measurement. (Magn. Reson. Med. 62, 520-526, 2009) 5. Measurement of Glutamate (Glu) in Anterior Cingulate of Chronic Cocaine Users using TE-Averaged PRESS at 3T with an Optimized Quantification Strategy The present study examined whether this ACC hypoactivity is associated with altered glutamate (Glu), the primary excitatory neurotransmitter in the central nervous system (CNS), which has been recently implicated in drug addiction. Fourteen chronic cocaine addicts and 14 matched healthy volunteers were examined using 1H magnetic resonance spectroscopy at 3T. We found that Glu/tCr was significantly lower in chronic cocaine users compared to control subjects and was significantly correlated with years of cocaine use. Glu/tCr was also positively correlated with NAA/tCr. These findings suggest a metabolic/ neurotransmitter dysregulation associated with cocaine addiction and support a possible therapeutic intervention strategy aimed at normalizing the Glu transmission and function in the treatment of cocaine addiction. (Psychiatry Research: Neuroimaging, in press) 6. Unbiased group-wise image registration and its applications to T1-weighted, diffusion Tensor and functional images In this study, an implicit reference group-wise (IRG) registration with a small deformation, linear elastic model was proposed. The implicit reference is estimated during IRG registration eliminating the bias associated with selecting a specific reference image. Registration performance was evaluated using segmented T1-weighted magnetic resonance images, DTI and fMRI images. IRG registration produces consistent correspondence between images in a group at the cost of slightly reduced pair-wise accuracy. IRG spatial normalization of the fractional anisotropy (FA) maps of DTI is shown to have smaller FA variance compared with G2R methods using the same elastic registration model. Analyses of fMRI data sets with sensorimotor and visual tasks show that IRG registration, on average, increases the statistical detectability of brain activation compared to G2R registration. (NeuroImage, 2009, 47, p1341-1351) 7. Higher-order diffusion MRI registration using orientation distribution functions represented by spherical harmonics We propose a linear-elastic registration method to register diffusion-weighted MRI data sets by mapping their diffusion orientation distribution functions (ODFs). The registration method is based on mapping the ODF maps represented by spherical harmonics which yield analytic solutions and reduce the computational complexity. ODF reorientation is required to maintain the consistency with transformed local fiber directions. Experimental results show that the elastic registration improved the affine alignment by further reducing the ODF shape difference;reorientation during the registration produced registered ODF maps with more consistent principle directions compared to registrations without reorientation or simultaneous reorientation. (Information Processing in Medical Imaging, 21, p.626-637, 2009)